Two geographic subpopulations (Eastern and Western) of the Asturian Bermeya goat were analysed using 27 microsatellites. A total of 122 individuals of Bermeya, Guadarrama, Alpine and Saanen goat breeds were genotyped. The Eastern and Western Bermeya subpopulations had expected heterozygosity values lower than 0.6 and within-subpopulations molecular coancestry values of 0.419, thus illustrating a high between individuals genetic identity. The rarefacted average number of alleles per locus found in both the Eastern and the Western Bermeya subpopulations were the lowest in the dataset (3.8 and 3.9, respectively). The higher between-populations molecular coancestry values was found for the pair Eastern Bermeya-Guadarrama (0.388 ± 0.006), thus reflecting the introgression of the Pyrenean-type goat into Eastern Asturias. This parameter between the two Bermeya subpopulations was of 0.371 ± 0.007. It could be recommended the implementation of different conservation strategies for each of the geographic subpopulations of Bermeya goat.